Systems and methods for monitoring the amplification and dissociation behavior of DNA molecules

ABSTRACT

The present invention relates to systems and methods for monitoring the amplification of DNA molecules and the dissociation behavior of the DNA molecules.

This application is a divisional of and claims priority to U.S. patentapplication Ser. No. 13/669,330, filed on Nov. 5, 2012, which is acontinuation of and claims priority to U.S. patent application Ser. No.12/552,645, filed on Sep. 2, 2009, now U.S. Pat. No. 8,306,294, which isa continuation of and claims priority to U.S. patent application Ser.No. 11/947,237, filed on Nov. 29, 2007, now U.S. Pat. No. 7,593,560,which claims the benefit of U.S. Provisional Patent Application Ser. No.60/861,712, filed on Nov. 30, 2006, each of which are incorporatedherein by reference in their entirety.

BACKGROUND

Field of the Invention

The present invention relates to systems and methods for monitoring theamplification of DNA molecules and the dissociation behavior of the DNAmolecules.

Discussion of the Background

The detection of nucleic acids is central to medicine, forensic science,industrial processing, crop and animal breeding, and many other fields.The ability to detect disease conditions (e.g., cancer), infectiousorganisms (e.g., HIV), genetic lineage, genetic markers, and the like,is ubiquitous technology for disease diagnosis and prognosis, markerassisted selection, correct identification of crime scene features, theability to propagate industrial organisms and many other techniques.Determination of the integrity of a nucleic acid of interest can berelevant to the pathology of an infection or cancer. One of the mostpowerful and basic technologies to detect small quantities of nucleicacids is to replicate some or all of a nucleic acid sequence many times,and then analyze the amplification products. Polymerase chain reaction(PCR) is a well-known technique for amplifying DNA.

With PCR, one can quickly produce millions of copies of DNA startingfrom a single template DNA molecule. PCR includes a three phasetemperature cycle of denaturation of the DNA into single strands,annealing of primers to the denatured strands, and extension of theprimers by a thermostable DNA polymerase enzyme. This cycle is repeateda number of times so that at the end of the process there are enoughcopies to be detected and analyzed. For general details concerning PCR,see Sambrook and Russell, Molecular Cloning—A Laboratory Manual (3rdEd.), Vols. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.(2000); Current Protocols in Molecular Biology, F. M. Ausubel et al.,eds., Current Protocols, a joint venture between Greene PublishingAssociates, Inc. and John Wiley & Sons, Inc., (supplemented through2005) and PCR Protocols A Guide to Methods and Applications, M. A. Inniset al., eds., Academic Press Inc. San Diego, Calif. (1990).

In some applications, it is important to monitor the accumulation of DNAproducts as the amplification process progresses. Real-time PCR refersto a growing set of techniques in which one measures the buildup ofamplified DNA products as the reaction progresses, typically once perPCR cycle. Monitoring the amplification process over time allows one todetermine the efficiency of the process, as well as estimate the initialconcentration of DNA template molecules. For general details concerningreal-time PCR see Real-Time PCR: An Essential Guide, K. Edwards et al.,eds., Horizon Bioscience, Norwich, U.K. (2004).

More recently, a number of high throughput approaches to performing PCRand other amplification reactions have been developed, e.g., involvingamplification reactions in microfluidic devices, as well as methods fordetecting and analyzing amplified nucleic acids in or on the devices.Thermal cycling of the sample for amplification is usually accomplishedin one of two methods. In the first method, the sample solution isloaded into the device and the temperature is cycled in time, much likea conventional PCR instrument. In the second method, the sample solutionis pumped continuously through spatially varying temperature zones. See,for example, Lagally et al. (Anal Chem 73:565-570 (2001)), Kopp et al.(Science 280:1046-1048 (1998)), Park et al. (Anal Chem 75:6029-6033(2003)), Hahn et al. (WO 2005/075683), Enzelberger et al. (U.S. Pat. No.6,960,437) and Knapp et al. (U.S. Patent Application Publication No.2005/0042639).

Once there are a sufficient number of copies of the original DNAmolecule, the DNA can be characterized. One method of characterizing theDNA is to examine the DNA's dissociation behavior as the DNA transitionsfrom double stranded DNA (dsDNA) to single stranded DNA (ssDNA) withincreasing temperature. The process of causing DNA to transition fromdsDNA to ssDNA is sometimes referred to as a “high-resolutiontemperature (thermal) melt (HRTm)” process, or simply a “high-resolutionmelt” process.

Accordingly, what is desired is a system for monitoring the DNAamplification process and for determining the DNA's dissociationbehavior.

SUMMARY OF THE INVENTION

The present invention relates to systems and methods for performing andmonitoring real-time PCR and HRTm analysis.

In one aspect, the present invention provides a method that includes thesteps of: introducing a sample of a solution comprising nucleic acidinto a microchannel; forcing the sample to move though the channel;defining a first window of a pixel array of an image sensor; defining asecond window of the pixel array, wherein the center of the secondwindow is spaced apart from the center of the first window; and whilethe sample is moving through the microchannel, performing the steps of:(a) exposing the first window of the pixel array to light emitted fromthe sample at a time when the sample is within a field of view of firstwindow and then selectively outputting first image data from the pixelarray, wherein the step of selectively outputting the first image datafrom the pixel array comprises outputting data from only the firstwindow of the pixel array; and (b) after performing step (a), exposingthe second window of the pixel array to light emitted from the sample ata time when the sample is within a field of view of second window andthen selectively outputting second image data from the pixel array,wherein the step of selectively outputting the second image data fromthe pixel array comprises outputting data from only the second window ofthe pixel array. The step of defining the second window may occur afterstep (a).

In some embodiments, when the step of exposing the first window of thepixel array to light emitted from the sample is performed, the center ofthe first window corresponds substantially to the center of the sample,and when the step of exposing the second window of the pixel array tolight emitted from the sample is performed, the center of the secondwindow corresponds substantially to the center of the sample.

In some embodiments the size of the second window may be less than orgreater than the size of the first window, and the step of defining thesecond window includes processing the first image data to determinewhether the amount of light received at a pixel located at an edge ofthe first window exceeds or equals a predetermined threshold.

In some embodiments, the method may also include the steps of: receivingfrom a first sensor a first signal indicating that the sample has beendetected by the first sensor and receiving from a second sensor a secondsignal indicating that the sample has been detected by the secondsensor, wherein the first sensor is positioned to detect when the sampleenters the field of view of the image sensor and the second sensor ispositioned to detect when the sample leaves the field of view of theimage sensor.

In some embodiments, the step of defining the first window of the pixelarray comprises determining the size of the window, wherein thedetermination is based, at least in part, on the length of the sample,and the step of defining the second window of the pixel array comprisesdetermining the location of the center of the second window, wherein thedetermination is based, at least in part, on a speed at which the samplemoves through the channel.

In another aspect, the present invention provides a system that includesthe following elements: a chip comprising a microchannel for receiving asample of solution comprising nucleic acid and for providing a path forthe sample to traverse; an image sensor having a pixel array, wherein atleast a portion of the microchannel is within a field of view of thepixel array; and an image sensor controller configured to: (a) read onlya first window of the pixel array at time when the sample is within afield of view of the first window, and (b) read only a second window ofthe pixel array at time when the sample is within a field of view of thesecond window, wherein the center of the second window is spaced apartfrom the center of the first window.

In another aspect, the present invention provides a method that includesthe following steps: introducing a sample of a solution comprisingnucleic acid into a channel; causing the sample to move though thechannel; defining a first window of a pixel array of an image sensor;defining a second window of the pixel array, wherein the center of thesecond window is spaced apart from the center of the first window; whilethe sample is moving through the microchannel, performing the steps of:(a) windowing the image sensor so that image data from the first windowis output to a data buffer, wherein said image data comprises data fromwhich the intensity of emissions from the sample can be determined; and(b) after performing step (a), windowing the image sensor so that imagedata from the second window is output to a data buffer, wherein saidimage data comprises data from which the intensity of emissions from thesample can be determined.

In yet another aspect, the present invention provides a method thatincludes the following steps: introducing a first sample of a solutioncomprising nucleic acid into a first channel; introducing a secondsample of a solution comprising nucleic acid into a second channel;causing the first sample to move though the first channel; causing thesecond sample to move though the second channel; defining a first windowof a pixel array of an image sensor, wherein at least a portion of thefirst channel is within the field of view of the first window; defininga second window of the pixel array, wherein at least a portion of thesecond channel is within the field of view of the second window andwherein the center of the second window is spaced apart from the centerof the first window; while the samples are moving through the respectivechannels, performing the steps of: (a) windowing the image sensor sothat image data from the first window is output to a data buffer,wherein said image data comprises data from which the intensity ofemissions from the first sample can be determined; and (b) afterperforming step (a), windowing the image sensor so that image data fromthe second window is output to a data buffer, wherein said image datacomprises data from which the intensity of emissions from the secondsample can be determined.

The above and other embodiments of the present invention are describedbelow with reference to the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated herein and form partof the specification, illustrate various embodiments of the presentinvention. In the drawings, like reference numbers indicate identical orfunctionally similar elements. Additionally, the left-most digit(s) of areference number identifies the drawing in which the reference numberfirst appears.

FIG. 1 illustrates a nucleic acid analysis system 100 according to anembodiment.

FIG. 2 is a top view of biochip 102 according to some embodiments.

FIG. 3 is a functional block diagram illustrating an embodiment of imageprocessing system 112.

FIG. 4 shows an exemplary pixel array 400.

FIG. 5 illustrates a process according to an embodiment.

FIG. 6 pictorially illustrates some of the steps of the process shown inFIG. 5.

FIG. 7 shows a first window of a pixel array and a second window of thepixel array.

FIG. 8 pictorially illustrates some of the steps of the process shown inFIG. 5.

FIG. 9 pictorially illustrates a process according to an embodiment.

FIG. 10 pictorially illustrates a process according to an embodiment.

FIG. 11 is a flow chart illustrating a process according to anotherembodiment.

FIG. 12 pictorially illustrates some of the steps of the process shownin FIG. 11.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

Referring to the drawings, FIG. 1 illustrates a nucleic acid analysissystem 100 according to an embodiment. As shown in FIG. 1, system 100includes a microfluidic biochip 102. FIG. 2 is a top view of biochip 102according to some embodiments. As shown in FIG. 2, biochip 102 includesa number of microfluidic channels 202. In the example shown, there are 4microfluidic channels (i.e., channels 202 a,b,c,d), but it iscontemplated that chip 102 may have more or less than 4 channels.

In some embodiments, when system 100 is in use, at least one channel 202receives a sample (or “bolus”) of a solution containing real-time PCRreagents. A force may be used to cause the bolus to travel through thechannel 202 and a thermal generating apparatus 114 may be used to cyclethe temperature of the bolus as described above while the bolus movesthrough the channel 202. One system and method for performing PCR in amicrofluidic device is disclosed in U.S. patent application Ser. No.11/505,358, filed on Aug. 17, 2006, incorporated herein by reference.

As further shown in FIG. 1, analysis system 100 may further include animage sensor 108, a controller 110 configured to control image sensor108, and an image processing system 112 configured to process the imagedata produced by image sensor 108. Image sensor 108 may be implementedusing a CMOS image sensor, a CCD image sensor, or other image sensor.For example, in one embodiment, sensor 108 is a CMOS sensor with aneffective 12.7 mega pixel resolution and having a size of 36×24 mm,which is available from Canon Inc.

Referring now to FIG. 3, FIG. 3 is a functional block diagramillustrating an embodiment of image processing system 112. As shown inFIG. 3, system 112 receives data output from image sensor 108. System112 may include an amplifier 302 to amplify the data from image sensor108. In one non-limiting embodiment, amplifier 302 may amplify the datafor greater sensitivity. The amplified data may be converted to adigital signal by, for example, a 16 bit analog-to-digital (A/D)converter 304. In one embodiment, utilization of a 16 bit A/D converterprovides a high level of dynamic range and low end bit resolution. Thedigital signal output from A/D converter 304 may be processed by aframing circuit 306, which may be configured to store data producedduring an HRTm process in a zone 1 data buffer 308 and store dataproduced during a PCR process in a zone 2 data buffer 310. Aprogrammable data processor 312 may be programmed to process data inbuffers 310 and 312 to, among other things, determine and record theintensity of the fluorescence from samples that undergo the PCR and HRTmprocessing.

As is well known in the art of imaging, image sensor 108 may have anarray of pixels. Referring now to FIG. 4, FIG. 4 shows an exemplarypixel array 400. For the sake of clarity, pixel array 400 includes only400 pixels. However, it is well understood that the pixel array of imagesensor 108 may have over 1 million pixels. In at least one embodiment,image sensor 108, lens 140 and chip 102 are arranged so that at least asignificant portion of each channel of chip 102 is within the field ofview of the pixel array 400 of image sensor 108. Also, in at least oneexemplary embodiment the image sensor 108 has the ability to read out apredefined portion or “window” of the pixel array (this is known aswindowing). FIG. 4 shows an example window 402, which consists of pixels433, 434, 443 and 444. As is well known in the art, image sensor 108 mayhave the ability to read out only the pixels that make up window 402(i.e., to obtain image data from only those pixels within window 402).For example, image sensor 108 may have pixel-row and pixel-column selectcircuits that enable one to read out only a particular window.Embodiments of the present invention can make use of this feature asdescribed below.

Referring now to FIG. 5, FIG. 5 is a flow chart illustrating a process500 according to an embodiment of the invention. Process 500 may beginin step 502, where a first sample of a solution comprising nucleic acidis introduced into a channel of chip 102 (for the sake of discussion wewill assume the sample is introduced into channel 202 a). In step 504, asecond sample of a solution comprising nucleic acid is introduced intoanother channel 202 of chip 102 (for the sake of discussion we willassume the sample is introduced into channel 202 b). Steps 502 and 504are illustrated in FIG. 6, which shows the first sample (i.e., sample601) in channel 202 a and shows the second sample (i.e., sample 602 inchannel 202 b). In step 506, a pressure force is applied to samples 601and 602 causing them to move through channels 202 a,b, respectively.

In step 508, a first window of pixel array 400 is defined such that atleast a portion of channel 202 a is within the field of view of thefirst window. In step 510, a second window of pixel array 400 is definedsuch that at least a portion of channel 202 b is within the field ofview of the second window and such that the center of the second windowis spaced apart from the center of the first window. Steps 508 and 510are illustrated in FIG. 7, which shows a first window 701 of pixel array400 and a second window 702 of pixel array 400.

While sample 601 moves through the field of view of window 701, step 512may be performed. Similarly, while sample 601 moves through the field ofview of window 701, step 520 may be performed. In step 512 thetemperature of sample 601 is cycled a number of times to achieveamplification of the nucleic acid present within sample 601 and in step520 the temperature of sample 602 is cycled to achieve amplification ofthe nucleic acid present within sample 602.

While steps 512 and 520 are being performed, steps 514 and 522 areperformed. In step 514, controller 110 windows image sensor 108 so thatimage data from window 701 is output to a data buffer and in step 516the image data is processed by image processing system 112. This imagedata comprises data from which the intensity of emissions from sample601 can be determined because when step 514 is performed, sample 601 iswithin the field of view of window 701, as illustrated in FIG. 8.Similarly, in step 522, controller 110 windows image sensor 108 so thatimage data from window 702 is output to a data buffer and in step 524the image data is processed by image processing system 112. This imagedata comprises data from which the intensity of emissions from sample602 can be determined because when step 522 is performed, sample 602 iswithin the field of view of window 702, as illustrated in FIG. 8. Asshown in FIG. 8, the width of windows 701 and 702 may be configured tobe slightly greater than the width of the respective channels (e.g., thewidth of window 701 may be equal to the pixel width of channel 202 aplus not more than several pixels).

As illustrated in FIG. 5, steps 514, 516, 522 and 524 may be repeated.

In some embodiments, prior to performing steps 514 and 522 again,windows 701 and 702 may be redefined. For example, windows 701 and/or702 may be made smaller so that less image data is transferred to thedata buffers on subsequent performance of step 514 and/or 522. In someembodiments, the window may be redefined so that the size of the windowis equal to the pixel size of the sample plus a few pixels, and thecenter of the window corresponds substantially to the location of thecenter of the sample.

To determine the pixel size of the sample, image processing system 112may be programmed to determine the pixels of pixel array that receivedat least a predetermined threshold of light from the sample. The windowmay then be defined to include those pixels plus, for each pixel, notmore than a predetermined number of neighboring pixels (e.g., not morethan about 5 neighboring pixels). This process is illustrated in FIG. 9.As shown in FIG. 9, the shaded pixels represent the pixels that receivedat least a predetermined amount of light from the sample during apredetermined integration period. Given this information, a window canbe defined to include not only these pixels, but also neighboring pixelsfor each pixel. Such a window 990 is shown in FIG. 9. As illustrated,window 990 includes not only not only the pixels that received at leastthe predetermined amount of light, but also two neighboring pixels foreach said pixel.

In one embodiment, to determine the point of the pixel array 400 thatcorresponds to the location of the center of the sample 601 at somespecific point in time, processing system 112 may compute the locationbased on knowledge of the location of the center of the sample 601 atsome previous point in time (e.g., the point in time when step 514 waslast performed), the average velocity of the sample during the timeperiod between the specific point in time and the previous point intime, and the time difference between the specific point in time and theprevious point in time. The location of the center of the sample 601 atsome previous point in time and the average velocity of the sample maybe known or may be derived from image data captured by image sensor 108.This process is illustrated in FIG. 10.

FIG. 10 shows a first group of pixels that received at least apredetermined amount of light from the sample at time t1. Pixel 1001 isin the center of this group of pixels. With this information, the pointof pixel array 400 that corresponds to the location of the center of thesample at time t2 can be determined using the following formula:S*(t2−t1), where s is the speed of the sample as it moves through thechannel in units of pixels/unit of time. For example if t2−t1 equals 1second and s equals 5 pixels per second and one knows the sample movesin the direction of arrow 1090, then one can determine that at time t2the center of the sample will be at pixel 1099.

Referring now to FIG. 11, FIG. 11 is a flow chart illustrating a process1100 according to an embodiment of the invention. Process 1100 may beginin step 1102, where a sample of a solution comprising nucleic acid isintroduced into a channel of chip 102. In step 1104, a force is appliedto the sample causing it to move through the channel.

While the sample is within at least some portion of the channel, step1110 is performed. In step 1110 the temperature of the sample is cycleda number of times to achieve amplification of the nucleic acid presentwithin sample.

While step 1110 is being performed, the following steps are performed.In step 1111 a window of pixel array 400 is defined such that at someparticular point in time the sample will be in the field of view of thewindow. Preferably, the window is sized and positioned such that thewindow is substantially equal to the pixel size of the sample (e.g., thepixel size of the sample plus a few pixels), and such that at theparticular point in time the center of the window correspondssubstantially to the location of the center of the sample. When theparticular point in time occurs, step 1112 is performed. In step 1112,the window receives emissions from the sample and then controller 110windows image sensor 108 so that image data from the window is output toa data buffer. Preferably, in step 1112 image sensor 108 is windowedsuch that only the image data from the window is output to the databuffer. This image data comprises data from which the intensity ofemissions from the sample can be determined. In step 1114, the imagedata may be processed by image processing system 112.

As illustrated in FIG. 11, steps 1111 and 1112 may be repeated.

Process 1100 is pictorially illustrated in FIG. 12, which shows a firstwindow 1201 of pixel array 400 and a second window 1202 of pixel array400. Window 1201 is defined the first time step 1111 is performed andwindow 1202 is defined the second time step 1111 is performed. As shownin FIG. 12, a window follows the sample by keeping track of the locationof the sample. Thus, by keeping track of the location of the sample, oneneed not read out the entire pixel array 400 in order to obtaininformation about a sample, rather one need only read out a small windowof the pixel array.

While various embodiments of the present invention have been describedabove, it should be understood that they have been presented by way ofexample only, and not limitation. Thus, the breadth and scope of thepresent invention should not be limited by any of the above-describedexemplary embodiments.

Additionally, while the processes described above are shown as asequence of steps, this was done solely for the sake of illustration.Accordingly, it is contemplated that some steps may be added, some stepsmay be omitted, and the order of the steps may be re-arranged.

Additional features are disclosed in the document attached hereto asappendix A.

For the claims below the words “a” and “an” should be construed as “oneor more.”

What is claimed is:
 1. A DNA analysis system, comprising: a chipcomprising a microchannel for receiving a sample of solution comprisingnucleic acid and for providing a path for the sample to traverse; animage sensor having a pixel array, wherein at least a portion of themicrochannel is within a field of view of the pixel array; and an imagesensor controller configured to change an area of the pixel array for(a) reading a first area of the pixel array at a time when the sample iswithin a field of view of the first area, thereby producing first imagedata, and for (b) reading a second area of the pixel array at a timewhen the sample is within a field of view of the second area, wherein acenter of the first area is spatially separated from a center of thesecond area, wherein the image sensor controller is configured to usethe first data to determine the size of the second area and the size ofthe second area is less than the size of the first area.
 2. The systemof claim 1, wherein the image sensor controller is configured to processthe first image data to determine whether the amount of light receivedat a pixel located at an edge of the first area exceeds or equals apredetermined threshold.
 3. The system of claim 1, further comprising afirst sample sensor positioned to detect the sample when the sampleenters or is about to enter the field of view of the image sensor andconfigured to output a signal in response to detecting the sample. 4.The system of claim 3, further comprising a second sample sensorpositioned to detect the sample when the sample leaves or is about toleave the field of view of the image sensor and configured to output asignal in response to detecting the sample.
 5. A DNA analysis device,comprising: an image sensor having a pixel array, wherein at least aportion of a microchannel providing a path for a sample of solutioncomprising nucleic acid to traverse is within a field of view of thepixel array; and an image sensor controller configured to change an areaof the pixel array for (a) reading a first area of the pixel array at atime when the sample is within a field of view of the first area,thereby producing first image data, and for (b) reading a second area ofthe pixel array at a time when the sample is within a field of view ofthe second area, wherein a center of the first area is spatiallyseparated from a center of the second area, wherein the image sensorcontroller is configured to use the first data to determine the size ofthe second area and the size of the second area is less than the size ofthe first area.
 6. The device of claim 5, wherein the image sensorcontroller is configured to process the first image data to determinewhether the amount of light received at a pixel located at an edge ofthe first area exceeds or equals a predetermined threshold.
 7. Thedevice of claim 5, further comprising a first sample sensor positionedto detect the sample when the sample enters or is about to enter thefield of view of the image sensor and configured to output a signal inresponse to detecting the sample.
 8. The device of claim 7, furthercomprising a second sample sensor positioned to detect the sample whenthe sample leaves or is about to leave the field of view of the imagesensor and configured to output a signal in response to detecting thesample.